1-109279521-G-A

Position:

• chr1-109279521-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.638 in 152,134 control chromosomes in the GnomAD database, including 35,003 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.64 (34952 hom., cov: 33)
  • Exomes 𝑓: 0.83 (51 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

(HGNC:):

PSRC1 (HGNC:24472): (proline and serine rich coiled-coil 1) This gene encodes a proline-rich protein that is a target for regulation by the tumor suppressor protein p53. The encoded protein plays an important role in mitosis by recruiting and regulating microtubule depolymerases that destabalize microtubules. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Apr 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSRC1	NM_001032291.3	c.*632C>T		downstream_gene_variant		ENST00000369909.7	NP_001027462.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSRC1	ENST00000369909.7	c.*632C>T		downstream_gene_variant		1	NM_001032291.3	ENSP00000358925.2

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96929 AN: 151864 Hom.: 34950 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.686

GnomAD4 exome AF: 0.829 AC: 126 AN: 152 Hom.: 51 Cov.: 0 AF XY: 0.845 AC XY: 71 AN XY: 84

Gnomad4 AMR exome AF: 0.500

Gnomad4 FIN exome AF: 0.828

Gnomad4 NFE exome AF: 0.875

GnomAD4 genome AF: 0.638 AC: 96951 AN: 151982 Hom.: 34952 Cov.: 33 AF XY: 0.642 AC XY: 47674 AN XY: 74286

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.689

Alfa AF: 0.684 Hom.: 4917

Bravo AF: 0.619

Asia WGS AF: 0.810 AC: 2818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1277930; hg19: chr1-109822143;